Instruct Course on the development of image processing workflows in streaming and structural data analysis components for Electron Microscopy. Madrid, October 26-29, 2020. (Online edition)

Venue

Remote course (TBA)
October 26-29, 2020 from 15.00-18.00 CET

Overall aims and course outline

Electron microscopy is a well-established and rapidly growing structural technique. There are some consolidated software packages like Relion, Xmipp, Cistem, Eman, IMOD, TomoJ, … that address the image processing steps required for single particle analysis and electron tomography. There are also independent software tools that address a particular and isolated task like movie alignment, CTF determination, particle picking, etc. Software platforms like Scipion facilitate the integration of packages from many different laboratories, and promote the cross-checking of the results by alternative methods. Additionally, Scipion keeps track of all the operations, parameters and steps undertaken from the raw data to the final maps and models, promoting, in this way, the reproducibility of the results. Scipion is used at individual laboratories and at general cryoEM Facilities worldwide. Scipion is quickly expanding to cover the atomic modelling steps and, more recently, tomography software. 


This course will show how to integrate into Scipion any software related to electron microscopy data analysis. You will learn the basic Scipion architecture and to construct a fully functional plugin containing the main elements: protocols, viewers and wizards. The course is aimed at programmers, engineers, computational scientists, physicists, mathematicians, and in general to information technology related scientists with interest in integrating their ideas or software into Scipion. Especially welcome are those developers of software packages or independent software tools for Electron Microscopy. It is suggested that attendees come with their own computer in which they can install software development tools.

 

Target Audience

Software developers interested in developing a Scipion plugin or integrating their software in Scipion.

Conditions

Remote course
Medium programming skills are required:

Python skills are desirable.

AWS machines might be provided by us.

If you want to use your own laptop for development instead of you may need:
– OS Linux (Ubuntu recommended)
CUDA (if you have a GPU)
– python3
– Conda or miniconda (optional, otherwise we will use virtualenv)

Contact

Lead contact:  
Carlos Oscar Sorzano
email. coss@cnb.csic.es

Pablo Conesa
email: pconesa@cnb.csic.es

Administrative Contact:
Blanca Benitez
email: blanca@cnb.csic.es

Tutors

I2PC staff: Carlos Oscar Sanchez-Sorzano (COSS), David Maluenda (DM), Jorge Jiménez (JJ), Pablo Conesa (PC), Roberto Marabini (RM), Yunior Fonseca (YF). 

Other tutors: José Miguel de la Rosa Trevín (JMRT from SciLifeLab in Stockholm), Grigory Sharov (GS from MRC-LMB in Cambridge)

Program

Guided practice where attendees will learn how to develop a Scipion plugin from scratch.

Day 1: 3h  (JJ)

 

Day 2: 3h (COSS)

Welcome (Jose María)
AWS
Install scipion
Pycharm configuration
Template plugin → hello world (plugin): (JJ)

Low pass filter a volume (protocol practice):

 

Objects: Pointers, Volume
Viewers: Show filtered volume +difference

 

Viewers/view
ImageHandler intro, list file formats supported

Tests:

 

Plugin structure: Modules: Protocols.
Objects: Scalars
Protocols

 

Datasets
Buildbot

 

Class methods: define params, insert steps, steps
Folder structure, path methods (getExtraPath,…)

   

Day 3: 3h (RM)

Day 4: 3h (DM)

Set stats protocol, analyse mean and std of images:

Streaming: EMPIAR downloader:

 

Objects: Sets, Particles
Extending the model with own attributes
ImageHandler → numpy integration.
gpu threads, mpi. USE_GPU and GPU_LIST protocol params.
Customizing ShowJ – ProtocolViewer

 

run.db
Sets persistence (sqlite, open set, closed set)

 

 

Day 5: 3h: (PC)

Wizards: demonstrate a simple mask wizard?

Plugin class:

   

Variables
Environment
Binaries installation (Conda environments, void.tgz)

 

Releasing

 

Sonarcloud
Upload to pypi
Github action

Key dates:

01 – 30 September, 2020: Submission of the course application

01 – 15 October, 2020: Communication of awarded applications  

REGISTRATION

Registration will be free for all attendees.

Fill  your application here

 
This course is funded by Instruct – ERIC, an Integrated Structural Biology Infrastructure for Europe

.